A Three-Dimensional Stereotaxic MRI Brain Atlas of the Cichlid Fish Oreochromis mossambicus

The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system.

Desenvolvimento de um fantoma cerebral para ressonância magnética

O controlo da qualidade em ressonância magnética (RM) passa pela realização de diversos testes ao equipamento e calibrações diárias, onde os fantomas desempenham um papel fundamental. Este trabalho teve como objetivo principal o desenvolvimento de um fantoma cerebral para um sistema de RM de intensidade 3.0 Tesla. Com base na literatura existente, escolheram-se como reagentes o cloreto de gadolínio (III) (GdCl3), a agarose, e o gelificante carragena, tendo sido ainda acrescentado o conservante químico azida de sódio (NaN3) de forma a inibir a degradação da solução. Realizaram-se vários testes com diferentes concentrações dos materiais selecionados até obter as misturas adequadas a suscetibilidade magnética das substâncias branca e cinzenta cerebrais. Os tempos de relaxação T1 das diversas substâncias desenvolvidas foram medidos, apresentando o fantoma final uns tempos de T1 de 702±10 ms, quando a concentração de GdCl3 foi de 100 µmol (substância branca) e 1179±23 ms quando a concentração foi de 15 µmol (substância cinzenta). Os valores de T1 do fantoma foram comparados estatisticamente com os tempos de relaxação conseguidos a partir de um cérebro humano, obtendo-se uma correlação de 0.867 com significância estatística. No intuito de demonstrar a aplicabilidade do fantoma, este foi sujeito a um protocolo de RM, do qual constaram as sequências habitualmente usadas no estudo cerebral. Como principais resultados constatou-se que, nas sequências ponderadas em T1, o fantoma apresenta uma forte associação positiva (rs > 0.700 p = 0.072) com o cérebro de referência, ainda que não sejam estatisticamente significativos. As sequências ponderadas em T2 demonstraram uma correlação positiva moderada e fraca, sendo a ponderação densidade protónica a única a apresentar uma associação negativa. Desta forma, o fantoma revelou-se um ótimo substituto do cérebro humano. Este trabalho culminou na criação de um modelo cerebral tridimensional onde foram individualizadas as regiões das substâncias branca e cinzenta, de forma a posteriormente serem preenchidas pelas correspondentes substâncias desenvolvidas, obtendo-se um fantoma cerebral antropomórfico.

Natalizumab versus Interferon B-1b to prevent CDMS in patients with CIS and poor prognostic factors: research protocol

About 85% of multiple sclerosis (MS) cases start as clinically isolated syndrome (CIS).When patients present with a CIS, clinicians face with many questions, most of themrelated with prognosis and treatment. Thereby, patients with CIS have been focus ofresearch. Several studies have demonstrated a relationship between positive IgM lipidspecific oligoclonal band pattern in CSF and higher lesion load on MRI brain scan, higher number of relapses and greater disability, even at the first stages of the disease. On the other hand, no studies have used this previous evidence to treat with more aggressive disease modifying therapy in initial stages of disease course to prevent the earlier axonal damage. The aim of this study is to assess the most effective approved treatment for MS and current therapy for CIS patients presenting high risk to develop CDMS and with biomarkers of poor prognosis. Among this group of patients any disease activity will eventually lead to disability. Therefore, the earlier the treatment is initiated, the more effective to prevent disability will be. It is considered that “time lost is brain lost” and since once damage is established, there is no therapy to be regained later on. In this phase III clinical trial, 172 patients will be randomized 1:1 to receive Interferon β-1b or natalizumab over 96 weeks. Time to develop clinical definitive multiple sclerosis (CDMS) will be included as primary endpoint. Other secondary endpoints will include clinical data, magnetic resonance imaging (MRI) measurements and quality of life tests

Natalizumab versus Interferon B-1b to prevent CDMS in patients with CIS and poor prognostic factors: research protocol

About 85% of multiple sclerosis (MS) cases start as clinically isolated syndrome (CIS).When patients present with a CIS, clinicians face with many questions, most of themrelated with prognosis and treatment. Thereby, patients with CIS have been focus ofresearch. Several studies have demonstrated a relationship between positive IgM lipidspecific oligoclonal band pattern in CSF and higher lesion load on MRI brain scan, higher number of relapses and greater disability, even at the first stages of the disease. On the other hand, no studies have used this previous evidence to treat with more aggressive disease modifying therapy in initial stages of disease course to prevent the earlier axonal damage. The aim of this study is to assess the most effective approved treatment for MS and current therapy for CIS patients presenting high risk to develop CDMS and with biomarkers of poor prognosis. Among this group of patients any disease activity will eventually lead to disability. Therefore, the earlier the treatment is initiated, the more effective to prevent disability will be. It is considered that “time lost is brain lost” and since once damage is established, there is no therapy to be regained later on. In this phase III clinical trial, 172 patients will be randomized 1:1 to receive Interferon β-1b or natalizumab over 96 weeks. Time to develop clinical definitive multiple sclerosis (CDMS) will be included as primary endpoint. Other secondary endpoints will include clinical data, magnetic resonance imaging (MRI) measurements and quality of life tests

Automatic Brain Extraction in Fetal MRI using Multi-Atlas-based Segmentation

In fetal brain MRI, most of the high-resolution reconstruction algorithms rely on brain segmentation as a preprocessing step. Manual brain segmentation is however highly time-consuming and therefore not a realistic solution. In this work, we assess on a large dataset the performance of Multiple Atlas Fusion (MAF) strategies to automatically address this problem. Firstly, we show that MAF significantly increase the accuracy of brain segmentation as regards single-atlas strategy. Secondly, we show that MAF compares favorably with the most recent approach (Dice above 0.90). Finally, we show that MAF could in turn provide an enhancement in terms of reconstruction quality.

Whole-body MRI: comprehensive evaluation on a 48-channel 3T MRI system in less than 40 minutes. Preliminary results

OBJECTIVE: To evaluate a comprehensive MRI protocol that investigates for cancer, vascular disease, and degenerative/inflammatory disease from the head to the pelvis in less than 40 minutes on a new generation 48-channel 3T system. MATERIALS AND METHODS: All MR studies were performed on a 48-channel 3T MR scanner. A 20-channel head/neck coil, two 18-channel body arrays, and a 32-channel spine array were employed. A total of 4 healthy individuals were studied. The designed protocol included a combination of single-shot T2-weighted sequences, T1-weighted 3D gradient-echo pre- and post-gadolinium. All images were retrospectively evaluated by two radiologists independently for overall image quality. RESULTS: The image quality for cancer was rated as excellent in the liver, pancreas, kidneys, lungs, pelvic organs, and brain, and rated as fair in the colon and breast. For vascular diseases ratings were excellent in the aorta, major branch vessel origins, inferior vena cava, portal and hepatic veins, rated as good in pulmonary arteries, and as poor in the coronary arteries. For degenerative/inflammatory diseases ratings were excellent in the brain, liver and pancreas. The inter-observer agreement was excellent. CONCLUSION: A comprehensive and time efficient screening for important categories of disease processes may be achieved with high quality imaging in a new generation 48-channel 3T system.

Whole-body MRI: comprehensive evaluation on a 48-channel 3T MRI system in less than 40 minutes. Preliminary results

OBJECTIVE: To evaluate a comprehensive MRI protocol that investigates for cancer, vascular disease, and degenerative/inflammatory disease from the head to the pelvis in less than 40 minutes on a new generation 48-channel 3T system. MATERIALS AND METHODS: All MR studies were performed on a 48-channel 3T MR scanner. A 20-channel head/neck coil, two 18-channel body arrays, and a 32-channel spine array were employed. A total of 4 healthy individuals were studied. The designed protocol included a combination of single-shot T2-weighted sequences, T1-weighted 3D gradient-echo pre- and post-gadolinium. All images were retrospectively evaluated by two radiologists independently for overall image quality. RESULTS: The image quality for cancer was rated as excellent in the liver, pancreas, kidneys, lungs, pelvic organs, and brain, and rated as fair in the colon and breast. For vascular diseases ratings were excellent in the aorta, major branch vessel origins, inferior vena cava, portal and hepatic veins, rated as good in pulmonary arteries, and as poor in the coronary arteries. For degenerative/inflammatory diseases ratings were excellent in the brain, liver and pancreas. The inter-observer agreement was excellent. CONCLUSION: A comprehensive and time efficient screening for important categories of disease processes may be achieved with high quality imaging in a new generation 48-channel 3T system.

Easy preoperative planning of deeply located brain lesions using external skin reference and 3-Dimensional surface MRI

Open skull surgery of deeply located intracerebral lesions requires precise determination of the treatment area in 3-dimensional (3-D) space. 3-D MRI can give important additional information in presurgical determination of the surgical approach to the target, taking into account highly functional brain areas and important vascular structures. The day before surgery, a grid composed of 9 tubings intersecting at 90° at 1 cm intervals and filled with a Q1SO4 solution is firmly attached to the skin of the patient’s head in the presumed region of the craniotomy. A 3-D turbo-FLASH sequence is then performed in the sagittal plane after intravenous Gd-DOTA injection on a IT Magnetom. 3-D surface reconstruction of the cortical gyri and sulci is performed. Once the gyri are identified, the 3-D program is then implemented in order to perform a color display of the cortical veins and of the tumor boundaries. The surgical access is then chosen by the surgeon, taking into account highly functional areas. Finally, the boundaries of the tumor are projected on the cortex reconstruction and on the external reference placed on the skin. The entry place for surgery as well as the size of craniotomy are drawn on the skin and the tubed grid is removed. The accuracy of this method tested in 9 patients with deeply located brain tumors or arteriovenous malformations was very satisfactory. In daily practice, this method is a valuable technique providing important clinical information in determining the shortest and safest way through the brain tissue, decreasing possible functional deficit and reducing craniotomy size in cases of difficult to access deep brain areas. Our method does not require a stereotactic frame permanently fixed to the head of the patient during surgery. © 1994 S. Karger AG, Basel.

Listeria brain abscess, Pneumocystis pneumonia and Kaposi's sarcoma after temozolomide.

BACKGROUND: A 55-year-old man with glioblastoma multiforme was treated with continuous, dose-dense temozolomide. This therapy was curtailed after three cycles because of nausea, asthenia, and neuropsychological deterioration. During a subsequent course of radiotherapy, the patient developed fever, headaches, and cutaneous lesions. INVESTIGATIONS: Physical examination, cerebral MRI, brain biopsy, skin biopsy, immunohistochemistry, bronchoscopy with bronchoalveolar lavage, and laboratory tests. DIAGNOSIS: Severe temozolomide-induced immunosuppression, exacerbated by corticosteroids, with profound T-cell lymphocytopenia and simultaneous opportunistic infections with Pneumocystis jiroveci pneumonia, brain abscess with Listeria monocytogenes, and cutaneous Kaposi's sarcoma. MANAGEMENT: Discontinuation of temozolomide, discontinuation of radiotherapy, antibiotic treatment with amoxicillin and gentamicin, and administration of atovaquone and pentamidine.

Ultra-high Field (7 T) MRI and a Novel Robust Segmentation of Thalamic Nuclei on DWI for Gamma Knife Surgery Purposes: The Targeting of the Ventrointermediate Nucleus

Introduction: Gamma Knife surgery (GKS) is a noninvasive neurosurgical stereotactic procedure, increasingly used as an alternative to open functional procedures. This includes the targeting of the ventrointermediate nucleus of the thalamus (e.g., Vim) for tremor. Objective: To enhance anatomic imaging for Vim GKS using high-field (7 T) MRI and Diffusion Weighted Imaging (DWI). Methods: Five young healthy subjects and two patients were scanned both on 3 and 7 T MRI. The protocol was the same in all cases, and included: T1-weighted (T1w) and DWI at 3T; susceptibility weighted images (SWI) at 7T for the visualization of thalamic subparts. SWI was further integrated into the Gamma Plan Software® (LGP, Elekta Instruments, AB, Sweden) and co-registered with 3T images. A simulation of targeting of the Vim was done using the quadrilatere of Guyot. Furthermore, a correlation with the position of the found target on SWI and also on DWI (after clustering of the different thalamic nuclei) was performed. Results: For the 5 healthy subjects, there was a good correlation between the position of the Vim on SWI, DWI and the GKS targeting. For the patients, on the pretherapeutic acquisitions, SWI helped in positioning the target. For posttherapeutic sequences, SWI supposed position of the Vim matched the corresponding contrast enhancement seen at follow-up MRI. Additionally, on the patient's follow-up T1w images, we could observe a small area of contrast-enhancement corresponding to the target used in GKS (e.g., Vim), which belongs to the Ventral-Lateral-Ventral (VLV) nuclei group. Our clustering method resulted in seven thalamic groups. Conclusion: The use of SWI provided us with a superior resolution and an improved image contrast within the central gray matter, enabling us to directly visualize the Vim. We additionally propose a novel robust method for segmenting the thalamus in seven anatomical groups based on DWI. The localization of the GKS target on the follow-up T1w images, as well as the position of the Vim on 7 T, have been used as a gold standard for the validation of VLV cluster's emplacement. The contrast enhancement corresponding to the targeted area was always localized inside the expected cluster, providing strong evidence of the VLV segmentation accuracy. The anatomical correlation between the direct visualization on 7T and the current targeting methods on 3T (e.g., quadrilatere of Guyot, histological atlases, DWI) seems to show a very good anatomical matching.

Simulation-based evaluation of susceptibility distortion correction methods in diffusion MRI for connectivity analysis

Connectivity analysis on diffusion MRI data of the whole- brain suffers from distortions caused by the standard echo- planar imaging acquisition strategies. These images show characteristic geometrical deformations and signal destruction that are an important drawback limiting the success of tractography algorithms. Several retrospective correction techniques are readily available. In this work, we use a digital phantom designed for the evaluation of connectivity pipelines. We subject the phantom to a âeurooetheoretically correctâeuro and plausible deformation that resembles the artifact under investigation. We correct data back, with three standard methodologies (namely fieldmap-based, reversed encoding-based, and registration- based). Finally, we rank the methods based on their geometrical accuracy, the dropout compensation, and their impact on the resulting connectivity matrices.

A Genetic Algorithm for the selection of structural MRI features for classification of Mild Cognitive Impairment and Alzheimer's Disease

This work investigates the problem of feature selection in neuroimaging features from structural MRI brain images for the classification of subjects as healthy controls, suffering from Mild Cognitive Impairment or Alzheimer’s Disease. A Genetic Algorithm wrapper method for feature selection is adopted in conjunction with a Support Vector Machine classifier. In very large feature sets, feature selection is found to be redundant as the accuracy is often worsened when compared to an Support Vector Machine with no feature selection. However, when just the hippocampal subfields are used, feature selection shows a significant improvement of the classification accuracy. Three-class Support Vector Machines and two-class Support Vector Machines combined with weighted voting are also compared with the former and found more useful. The highest accuracy achieved at classifying the test data was 65.5% using a genetic algorithm for feature selection with a three-class Support Vector Machine classifier.

Smart histogram analysis applied to the skull-stripping problem in T1-weighted MRI

In this paper we address the "skull-stripping" problem in 3D MR images. We propose a new method that employs an efficient and unique histogram analysis. A fundamental component of this analysis is an algorithm for partitioning a histogram based on the position of the maximum deviation from a Gaussian fit. In our experiments we use a comprehensive image database, including both synthetic and real MRI. and compare our method with other two well-known methods, namely BSE and BET. For all datasets we achieved superior results. Our method is also highly independent of parameter tuning and very robust across considerable variations of noise ratio.

Segmentation of brain tumor images based on atlas-registration combined with a Markov-Random-Field lesion growth model

We present an automatic method to segment brain tissues from volumetric MRI brain tumor images. The method is based on non-rigid registration of an average atlas in combination with a biomechanically justified tumor growth model to simulate soft-tissue deformations caused by the tumor mass-effect. The tumor growth model, which is formulated as a mesh-free Markov Random Field energy minimization problem, ensures correspondence between the atlas and the patient image, prior to the registration step. The method is non-parametric, simple and fast compared to other approaches while maintaining similar accuracy. It has been evaluated qualitatively and quantitatively with promising results on eight datasets comprising simulated images and real patient data.

Volumetric and anatomical MRI for hypoxic-ischemic encephalopathy: relationship to hypothermia therapy and neurosensory impairments.

OBJECTIVE: To relate volumetric magnetic resonance imaging (MRI) findings to hypothermia therapy and neurosensory impairments. STUDY DESIGN: Newborns > or =36 weeks' gestation with hypoxic-ischemic encephalopathy who participated in the National Institute of Child Health and Human Development hypothermia randomized trial at our center were eligible. We determined the relationship between hypothermia treatment and usual care (control) to absolute and relative cerebral tissue volumes. Furthermore, we correlated brain volumes with death or neurosensory impairments at 18 to 22 months. RESULT: Both treatment groups were comparable before randomization. Total brain tissue volumes did not differ in relation to treatment assignment. However, relative volumes of subcortical white matter were significantly larger in hypothermia-treated than control infants. Furthermore, relative total brain volumes correlated significantly with death or neurosensory impairments. Relative volumes of the cortical gray and subcortical white matter also correlated significantly with Bayley Scales psychomotor development index. CONCLUSION: Selected volumetric MRI findings correlated with hypothermia therapy and neurosensory impairments. Larger studies using MRI brain volumes as a secondary outcome measure are needed.